execute_cibersort: Execute cibersort using Rserve

In hammerlab/rinfino: R-friendly client to run infino (http://github.com/hammerlab/infino)

Description

Execute cibersort using Rserve

Usage

execute_cibersort(input_file, output_file, absolute_mode = FALSE,
  tmpdir = tempdir(), cibersort_home = "~/cibersort",
  training_input = file.path(cibersort_home, "LM22.txt"),
  rserve_log = file.path(tmpdir, "Rserve_log.txt"),
  error_file = file.path(tmpdir, "cibersort_errors.txt"))

Arguments

input_file	path to input file on disk
output_file	path where output should be stored (on disk)
tmpdir	directory to use for intermediate results
cibersort_home	directory into which CIBERSORT_package.zip has been unzipped
training_input	path to gene signatures for cell types (defaults to LM22)
rserve_log	path in which to store Rserve stderr (contents printed on error)
error_file	path in which to store cibersort stderr (contents printed on error)

Value

cibersort results in a data.frame

Note

used by {run_cibersort} to call out to cibersort.

See Also

{run_cibersort} which takes an expdata object rather than a filepath

hammerlab/rinfino documentation built on May 27, 2019, 8:45 a.m.